The department has told principals that it will no longer support the intensive reading program for year 1 students after a report commissioned in 2015 found Reading Recovery was largely ineffective for most students.

Instead, the state government will redirect the more than $50 million it spends annually on the program into its $340 million literacy and numeracy strategy for kindergarten to year 10.

The president of the NSW Primary Principals' Association, Phil Seymour, said many principals were deeply concerned about the program being stopped.

"Principals tell me that it has been a great program for some kids and I know from the past two schools I was at, that it really works for some students," he said.

Mr Seymour said he was concerned that the government's literacy strategy would be too broad and young readers would miss out on necessary extra help.

"This really worries me because we know that early intervention is so important and with Reading Recovery we certainly saw some very good results," he said.

Reading Recovery is in about 960 NSW public schools and about 14 per cent of year 1 students who struggle with reading take part in the one-on-one program. It is also offered in many Catholic schools across the state.

Mr Seymour said he accepted that it was an expensive program but it had good outcomes and should not have been axed completely.

"Many principals have said to me that it should have continued in some form but there was almost no consultation," he said.

"The overall fear is that after 2018, we are not going to have the expert tutors for those kids who really struggle when it comes to reading."

A spokesman for the education minister, Rob Stokes, said: "The government has worked closely with the Primary Principals' Association over the past four months to ensure the withdrawal of central support for Reading Recovery was carried out with as little disruption to schools as possible.

"This process has been managed with the support of the PPA, specifically ensuring that there would be no changes to staff entitlement for primary schools this year."

The department's Centre for Education Statistics and Evaluation released its report two years ago which found that Reading Recovery was offered in too many schools and has few long-term benefits.

The report found that Reading Recovery should be restricted to the lowest-performing students and while it may have some impact on students who are really struggling with basic reading, the improvements are short-lived.

It is understood that schools will still be able to offer Reading Recovery in 2018 but without any support from the department and all funding will be redirected in 2019.

As part of its phase-out, a team of 50 literacy and numeracy experts will be recruited to support teachers, Mr Stokes said late last month.

The minister's spokesman said: "As of 2019, the $50 million currently provided to support Reading Recovery will be reinvested to ensure all students have the best opportunity to develop strong literacy and numeracy skills. All NSW public schools will also have the ability to carry out independent Reading Recovery programs if they so desire."